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- PDB-5y3m: Crystal structure of bovine TLR9 in complex with two DNAs (CpG DN... -

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Basic information

Entry
Database: PDB / ID: 5y3m
TitleCrystal structure of bovine TLR9 in complex with two DNAs (CpG DNA and TCGTTT DNA)
Components
  • DNA (5'-D(*TP*CP*GP*T)-3')
  • DNA (5'-D(P*GP*GP*CP*GP*TP*T)-3')
  • Toll-like receptor 9
KeywordsIMMUNE SYSTEM / Innate immunity / Toll-like receptor / Leucine-rich repeat / DNA binding
Function / homology
Function and homology information


regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / early phagosome / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / pattern recognition receptor activity ...regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / early phagosome / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of B cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of interleukin-6 production / positive regulation of type II interferon production / defense response to virus / lysosome / positive regulation of MAPK cascade / endosome / inflammatory response / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / plasma membrane
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / TIR domain profile. / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily ...Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / TIR domain profile. / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
DNA / Toll-like receptor 9
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOhto, U. / Shimizu, T.
CitationJournal: Immunity / Year: 2018
Title: Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation
Authors: Ohto, U. / Ishida, H. / Shibata, T. / Sato, R. / Miyake, K. / Shimizu, T.
History
DepositionJul 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-like receptor 9
E: DNA (5'-D(*TP*CP*GP*T)-3')
F: DNA (5'-D(*TP*CP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*CP*GP*TP*T)-3')
C: DNA (5'-D(P*GP*GP*CP*GP*TP*T)-3')
B: Toll-like receptor 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,57216
Polymers188,3596
Non-polymers2,21210
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13460 Å2
ΔGint-12 kcal/mol
Surface area59470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.177, 68.693, 153.535
Angle α, β, γ (deg.)90.00, 100.64, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 28 - 801 / Label seq-ID: 8 - 781

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BF

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Components

#1: Protein Toll-like receptor 9


Mass: 89323.531 Da / Num. of mol.: 2 / Fragment: UNP residues 25-817
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: TLR9 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q5I2M5
#2: DNA chain DNA (5'-D(*TP*CP*GP*T)-3')


Mass: 1790.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*GP*TP*T)-3')


Mass: 3066.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10%(w/v) PEG 4000 0.5M NaCl 0.1M Mes-NaOH pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.96 Å / Num. obs: 62911 / % possible obs: 99.9 % / Redundancy: 5.1 % / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WPE

3wpe


Resolution: 2.5→48.96 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.9 / SU B: 24.732 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.611 / ESU R Free: 0.281 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24427 3058 4.9 %RANDOM
Rwork0.22512 ---
obs0.22606 59852 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20.55 Å2
2---1.58 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 2.5→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11574 426 140 134 12274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211400
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9517063
X-RAY DIFFRACTIONr_angle_other_deg1.01326456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06351465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10623.295525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.282151988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2841586
X-RAY DIFFRACTIONr_chiral_restr0.0670.21963
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022530
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6172.2865875
X-RAY DIFFRACTIONr_mcbond_other0.6172.2855874
X-RAY DIFFRACTIONr_mcangle_it1.1463.4267335
X-RAY DIFFRACTIONr_mcangle_other1.1463.4267336
X-RAY DIFFRACTIONr_scbond_it0.5412.3896605
X-RAY DIFFRACTIONr_scbond_other0.5412.3896606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0093.5699729
X-RAY DIFFRACTIONr_long_range_B_refined2.28926.16712913
X-RAY DIFFRACTIONr_long_range_B_other2.27126.16312906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 46254 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 223 -
Rwork0.316 4412 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08790.0073-0.06470.11170.06050.13820.00720.00790.0053-0.00140.00790.0018-0.0211-0.0065-0.01510.12560.00660.01050.0933-0.00060.1135-0.42510.864740.2043
20.04630.1802-0.08370.7225-0.33960.16080.1041-0.07520.0493-0.0691-0.1520.16290.03990.12110.04790.077-0.02710.03970.1935-0.06710.1868-23.6331-21.337139.141
30.96260.72231.46272.5247-0.59723.7869-0.08370.1077-0.0192-0.18860.1487-0.0405-0.1830.0914-0.0650.1623-0.00860.04910.09620.03750.09428.2251-26.94052.2486
40.2515-0.86970.59633.0296-2.07441.4213-0.1871-0.06330.08630.19490.0861-0.339-0.136-0.13490.10110.06490.05870.02190.1733-0.07320.138839.2429-17.738330.8761
50.5776-0.273-0.15131.4752-0.18910.09420.0229-0.0243-0.0354-0.06740.0521-0.1399-0.0304-0.0187-0.0750.10020.02070.01570.1083-0.0340.17146.86-4.286564.3098
60.1073-0.03180.00150.09650.02490.1181-0.0104-0.01410.0116-0.00970.0205-0.01480.0304-0.009-0.01010.1105-0.0023-0.00250.0908-0.00390.126420.244-33.980732.7103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 1004
2X-RAY DIFFRACTION2E1 - 4
3X-RAY DIFFRACTION3F1 - 5
4X-RAY DIFFRACTION4D2 - 7
5X-RAY DIFFRACTION5C2 - 7
6X-RAY DIFFRACTION6B28 - 1004

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